About DOCK

DOCK was developed by Irwin D. "Tack" Kuntz, Jr., PhD and colleagues at UCSF. Please see the webpage at UCSF DOCK.

DOCK is a molecular docking program used in drug discovery. This program, given a protein active site and a small molecule, tries to predict the correct binding mode of the small molecule in the active site, and the associated binding energy. Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads. These leads are then further studied, and could eventually result in a new, marketable drug. DOCK is works well as a screening procedure for generating leads, but not nearly as well for optimization of those leads. Original DOCK used only rigid body docking, DOCK 4.0, however, introduced flexible ligand docking by either a)incremental construction or b)random search.

Incremental construction (aka anchor and grow) could be roughly described by a three step process:
1) rigid portion of ligand (anchor) is docked by geometrical methods
2) non-rigid segments added; energy minimized
3) the resulting configurations are 'pruned' and energy re-minimized, yielding the docked configurations

Random search method involves docking random conformations of ligand as independent rigid objects. The number of conformations allowed per rotatable bond is arbitrary and user controlled. The receptor is always held rigid in DOCK 4.0.

About Streptavidin & Biotin

Streptavidin is a tetrameric prokaryotic protein that binds the ligand biotin with an extremely high affinity. The streptavidin monomer is composed of eight antiparallel beta-strands which folds to give a beta barrel tertiary structure. A biotin binding-site is located at one end of each β-barrel, which has a high affinity as well as a high avidity for biotin. Four identical streptavidin monomers associate to give streptavidin’s tetrameric quaternary structure. The biotin binding-site in each barrel consists of residues from the interior of the barrel, together with a conserved Trp120 from neighbouring subunit. In this way, each subunit contributes to the binding site on the neighboring subunit, and so the tetramer can also be considered a dimer of functional dimers.

Biotin is a water soluble B-vitamin complex (organic small molecule) which is composed of an ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring. It is a co-enzyme that is required in the metabolism of fatty acids and leucine. It is also involved in gluconeogenisis.

Preparing the Enzyme and Ligand in Chimera

The part about downloading and building the initial receptor and ligand structures have already been covered as part of the AMBER tutorial. In this tutorial, we will be using the dockprep tool in chimera. You will need the following files:

Generation of Enzyme Surface, Spheres, and Grid for DOCK

Enzyme Surface

To generate an enzyme surface, first open the receptor pdb file with the hydrogen atoms removed (1DF8.rec.noH.pdb). Next, go to Actions -> Surface -> Show. Previous years, we had used the dms program to do this, but now chimera can generate the molecular surface itself. Note that for dock it is necessary to use the protein without hydrogens.

Recent versions of Chimera include a Write DMS tool that facilitates calculation of the molecular surface. Go to Tools -> Structure Editing -> Write DMS. Save the surface as 1DF8.receptor.dms.

The Write DMS tool will "roll" a small probe (default radius = 1.4 Angstroms = Size of a water molecule) over the surface of the enzyme and calculate the surface normal at each point. Note that this can also be accomplished with a separate dms program, as described in DOCK tutorials from previous years. DMS (distributed molecular surface) files are subsequently used as input for sphgen.

Spheres

To generate docking spheres, we need to use command line program called sphgen. To run the sphgen, we need a input file named INSPH.

1DF8.receptor.dms
R
X
0.0
4.0
1.4
1DF8.receptor.sph

1DF8.receptor.dms is the surface file we got from the previous step. (Change the file name to what you named the dms output something else). 1DF8.receptor.sph is the spheres file we want to generate in this step.

You can open the spheres file (1DF8_receptor.sph) with vim, as it is text file. There are over 700 spheres in this file. However, we're only interested in docking the ligand into the active site. Therefore we need to select only those spheres which are inside the active site, using sphere_selector command.

sphere_selector 1DF8.receptor.sph 1DF8.lig.mol2 10.0

1DF8.lig.mol2 is the ligand file we created earlier. sphere_selector will retain all spheres within 10.0A of the ligand as specified above. You should get a file called selected_spheres.sph. You can open it in vim. The number of spheres is drop down to 47 (check the first line).

Grid

The energy grid approximates the intermolecular interaction between the receptor and a dummy probe. This speeds up the evaluation of the intermolecular score between the receptor and the ligand.

Create a showbox.in file as following:

Y
5.0
selected_spheres.sph
1
1DF8.box.pdb

Type 'showbox < showbox.in'

Now create a grid.in file with a 0.3 grid spacing. The van der Waals components are a 6-9 instead of 6-12. It should look like this: